I do a transformation of the data removing couple of extra rows and columns and selecting the header is on 7th row. However, I have also tried the load using an edited file, where this transformation is not necessary, the same end result.

Is there possibly a limitation to maximum rows in the QlikView load script, that I haven't figured out?

BTW - this is not a "loss" of data. It just gets to a certain point where the msq quoting indicates and end of file. So you end up only getting the first XXX lines. It just doesn't get to the end of the file.